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Oncogenetica

The VUmc/CCA Section of Oncogenetics: at the Cross Road of Clinical Genetics and Cancer Research

The Cancer Center Amsterdam (CCA) houses one of the largest oncology research centers in the Netherlands, joining researchers and clinicians from the VU University Medical Center (VUmc) and the Academic Medical Center (AMC) in Amsterdam (https://www.amsterdamresearch.org/web/cancer-center-amsterdam/home-2.htm). CCA's mission is to improve treatment, life expectancy and quality of life for cancer patients and to reduce the impact of cancer on health care and society. At the CCA, excellent fundamental and translational research programs are intimately connected to clinical studies and clinical care.

Molecular Pathways Underlying Cancer Predispositions

The Oncogenetics Section of the Department of Clinical Genetics has a strong reputation in basic and bench-to-bedsite research on hereditary cancer-predisposition syndromes such as Retinoblastoma and Fanconi anemia (FA). Traditionally, research focussed on the identification of causal germline gene(s) that predispose to cancer. Recently, the section embraced a multi-disciplinary approach, combining next-gen DNA and RNA sequencing techniques, functional genomics, bio-informatics and cancer cell biology to study the molecular mechanisms of inheritable cancer. Research is directed at identifying key underlying cell biological processes, molecular signalling pathways and targetable vulnerabilities of predisposed cancers. A specific additional translational aspect in the case of hereditary cancers relates to the identification of specific strategies that help to prevent tumorigenesis. Three PI's work closely together on separate research themes: Dr. Job de Lange, Dr. Josephine Dorsman and Dr. Rob Wolthuis.

Research Theme 1

Functional Genomics of the Fanconi Anemia/BRCA Pathway

Project: Compensatory Mechanisms In Fanconi Pathway-Deficient Cancer Cells
Our work on FA genes shows how a rare disorder can expose a key DNA repair network. Here, we aim to further understand the consequences of defects in the FA/BRCA pathway in cancer and reveal vulnerabilities of FA cells that may be targeted in therapy. While such new therapies could be broadly applicable, particularly FA patients are in need of better treatment options. In FA patients, all cells are hypersensitive to DNA cross-linkers, rendering cancer treatment by conventional chemotherapy too toxic. Within our FA program, in which we work together with other basic researchers, clinicians and patient support groups, we offer three junior postdoctoral positions on distinct research projects funded by different granting agencies.

FA cells have a decreased fitness but nonetheless head and neck squamous cell carcinomas (HNSCCs), frequently arise in FA patients. This suggests that compensatory mechanisms exist that neutralize deleterious effects of loss of the FA pathway in FA tumor cells. In this functional-genomics project, cell lines from head and neck squamous cell carcinomas in FA patients were already screened in triplicate by genome-wide siRNA libraries, to identify genes that are lethal upon knock-down. We identified a list of statistically validated candidate genes that may operate in such compensatory mechanisms and that may drive tumor progression in FA patients. Functional studies of these genes, and the exploitation of their associated pathways for the design of new therapeutic strategies, are the main subjects of this project. The partnering with the groups of Ruud Brakenhoff and Victor van Beusechem at the CCA, and the group of Hein te Riele at the Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, guarantees an excellent research environment, easy access to relevant functional assays and materials, and optimal possibilities to translate findings into clinical applications.

Project: CRISPR-Cas9 Based Functional Genomics of Fanconi Anemia
The Fanconi Anemia Research Fund (FARF) is an American charity aimed at advancing FA research and supporting affected families. This project entails the development and and application of cutting-edge genomics and bioinformatics approaches, including the recently developed genome-wide CRISPR/Cas9 screens approaches to study unique vulnerabilities of squamous cell tumors from FA individuals. The partnering with the Luxembourg Centre for Systems Biomedicine is expected to boost the application of bioinformatics approaches to reveal functionally relevant networks. The focus of this project is to establish the CRISPR/Cas9 gene editing technology in the lab to efficiently introduce defined mutations or modulate expression in standard mammalian (primarily human) cell models for subsequent functional analysis. While setting up the methods, we will focus on pending questions in our ongoing FA- and the related oxygen tolerance lines of research. The project involves read-outs such as markers for mitophagy detection that can be followed by advanced fluorescence microscopy. 

Research Theme 2

Sister Chromatid Cohesion Weakness: A Cancer Vulnerability

Project:  Functional Genomics and Proteomics of Sister Chromatid Cohesion Defects
Sister chromatid cohesion is a process that keeps the newly replicated chromosomes together from the time of their synthesis in S phase until they separate during mitosis. We recently discovered that the cohesion between sister chromatids after DNA replication is critically impaired in cancer cell lines of several different subtypes. Moreover, in genome-wide synthetic lethality screens, we found that this so-called 'cohesion weakness' can serve as a unique vulnerability of cancer cells since it is not found in normal cells. As such, it could very well prove to be a specific and effective target for cancer treatment. Sensitivity to the synthetic lethal hits identified in our screen, as well as drugs that interfere with DNA replication, correlates with further enhanced cohesion weakness. In addition, we detected that cohesion weakness may also be caused by the induction of oncogenes in untransformed cells. These observations indicate that tumor cells have undergone oncogenic transformation at the expense of partial loss of cohesion, which can still be tolerated but may provide a therapeutically attractive vulnerability if cohesion is further abrogated. Exploitation of cohesion weakness as a targetable vulnerability of cancer cells requires an in-depth understanding of the specific mechanisms that direct sister chromatid cohesion during oncogenic transformation. We will use CRISPR-based genome wide screens to identify molecular pathways and vulnerabilities uniquely associated with sister chromatid cohesion defects. Advanced comparative analyses of the datasets will be performed in collaboration with Renee de Menezes , in order to identify hits and associated pathways. Using CRISPR-Cas9 based gene tagging, we GFP-labelled a sister chromatid cohesion subunit for cell biological and proteomic analyses of the cohesion ring and associated proteins, together with Connie Jimenez. Ultimately, this project will result in biomarkers and novel drug targets or drug combinations for cancer cells with cohesion weakness.

Project: Roberts Syndrome and Warsaw Breakage Syndrome: Cohesinopathies
Cohesinopathies are genetic instability syndromes associated with defects in the regulators and structural components of the cohesin complex . A cohesinopathy under study is Roberts syndrome (RBS),  in which the cohesion between the sister chromatids generated after DNA replication is disturbed due to a mutation in the putative acetyltransferase ESCO2, as discovered by our group in 2005. We also identified a novel cohesinopathy due to mutations in the helicase DDX11, which we designated Warsaw Breakage Syndrome (WABS) after the origin of the first affected individual. Also in this case we functionally corrected cell lines from the WABS patient for further characterization of the DDX11 protein. The WABS patient nicely connects our FA and RBS work, since the patient shows the cellular characteristics of both syndromes. In addition, DDX11 and FANCJ belong to the same family of iron-sulfur containing helicases. We are investigating the role of DDX11 and ESCO2 in sister chromatid cohesion and try to relate this function and that of other proteins involved in sister chromatid cohesion to aneuploidy and cancer.

Research Theme 3

Exploring Molecular Pathways and Targetable Vulnerabilities of Predisposed Cancers
Using CRISPR-CAs9, we engineer untransformed cell lines of relevant tissue origin with cancer predisposing mutations and cancer driving mutations, to  i) predict functional and clinical consequences of cancer gene mutations, ii) elucidate signal transduction pathways linked to cancer gene mutations, iii) identify biomarkers, including liquid biopsies of cancer-induced alterations in the blood of carriers of predisposing mutations, and iv) discover weak spots in cancer cells that render them sensitive to targeted therapies and tailor-designed drugs. For this we use functional genome-wide CRISPR screens of isogenic cell line pairs to elucidate the molecular and cellular functions of familial cancer genes and mutations, identify molecular mechanisms and reveal druggable pathways.

Project: The signal transduction pathways of the Birtt Hogg Dube gene FLCN.

Project: Comparative genomic analyses of cancer predisposing genes in different tissues of origin.

People

Dominique Akse, office manager
Janine Bakker, PhD student
Monique Corbin, PhD student
Josephine Dorsman, PI
Jesper Balk, research technician
Atiq Faramarz, PhD student
Iris Glykofridis, PhD student
Job de Lange, PI
Klaas de Lint, PhD student
Saskia van Mil, research technician
Govind Pai, postdoctoral researcher
Anneke Oostra, research technician
Martin Rooimans, research technician
Davy Rockx, research technician
Khash Roohollahi, PhD student
Lianne Vriend, postdoctoral researcher
Yne Waterham-de Vries, research technician
Rob Wolthuis, PI
Amr Zaini, postdoctoral researcher

Vacancy: PhD student in bio-informatics

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